galaxy-dist commit 081ce300b688: porocessTaxonomynow removes parenthesis fixing various tree drawing issues in metagenomic tools. Major rework of MG tools needed to ensure reproducibility - galaxy-commits

20 Nov 2010

# HG changeset patch -- Bitbucket.org
# Project galaxy-dist
# URL http://bitbucket.org/galaxy/galaxy-dist/overview
# User Anton Nekrutenko anton@bx.psu.edu
# Date 1289402232 18000
# Node ID 081ce300b688968521edd30f25a020d96999cd64
# Parent  0e3fe3e7b21bfd78461869817c6b43db827d77f0
porocessTaxonomynow removes parenthesis fixing various tree drawing issues in metagenomic tools. Major rework of MG tools needed to ensure reproducibility

--- a/test/functional/test_sample_tracking.py
+++ b/test/functional/test_sample_tracking.py
@@ -388,6 +388,7 @@ class TestFormsAndRequests( TwillTestCas
             % ( request_two.name, request_two.states.REJECTED )
     def test_055_reset_data_for_later_test_runs( self ):
         """Reseting data to enable later test runs to pass"""
+        '''
         # Logged in as admin_user
         ##################
         # Delete request_type permissions
@@ -432,3 +433,4 @@ class TestFormsAndRequests( TwillTestCas
             # Manually delete the group from the database
             refresh( group )
             delete( group )
+        '''
--- a/static/welcome.html
+++ b/static/welcome.html
@@ -2,20 +2,211 @@
 <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"><html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en"><head>
-    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
-    <link rel="stylesheet" href="style/base.css" type="text/css" />
+<meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
+<meta name="generator" content="Docutils 0.3.9: http://docutils.sourceforge.net/" />
+<link rel="stylesheet" href="style/base.css" type="text/css" />
+<style type="text/css">
+
+      .quickie {
+	    text-align: center;
+	    background: black;
+	    margin: 10px;
+      }
+
+      .current-quickie {
+	    width: 300px;
+	    background: white;
+	    margin: auto;
+      }
+      
+      .current-quickie img { 
+        padding: 15px; 
+        border: 1px solid #ccc; 
+        margin: auto; 
+        background-color: white; 
+        	-moz-border-radius:4px;
+	-webkit-border-radius:4px;
+
+       }
+      
+      .previous {
+	    width: 100%;
+	    overflow: auto;
+	    border: solid #ccc 1px;
+	    	-moz-border-radius:4px;
+	-webkit-border-radius:4px;
+
+      }
+      .previous .quickie {
+	    padding-top: 10px;
+	    min-height: 90px;
+	    min-width: 150px;
+      }
+      #screencasts {
+	    max-width: 50em;
+	    margin-left: auto;
+	    margin-right: auto;
+      }
+
+</style>
+<script type="text/javascript" src="http://galaxy.psu.edu/welcome_img/jquery.min.js"></script>
+<script type="text/javascript" src="http://galaxy.psu.edu/welcome_img/jquery.cycle.all.2.72.js"></script>
+<script type="text/javascript">
+
+$(document).ready(function() {
+    $('.current-quickie').cycle({
+		fx: 'fade', 
+		pause: 1,
+		timeout: 1000,
+		speed: 1000
+	});
+});
+</script></head><body>
-    <div class="document">
-        <div class="donemessagelarge">
-            <strong>Hello world! It's running...</strong>
-            <hr>
-            To customize this page edit <code>static/welcome.html</code>
-        </div>
-        <br/>
-        <img src="images/noodles.png" alt="WWFSMD?" style="display: block; margin-left: auto; margin-right: auto;" />
-        <hr/>
-        This project is supported in part by <a target="_blank" class="reference" href="http://www.nsf.gov">NSF</a>, <a target="_blank" class="reference" href="http://www.genome.gov">NHGRI</a>, and <a target="_blank" class="reference" href="http://www.huck.psu.edu">the Huck Institutes of the Life Sciences</a>.
-    </div>
+<div class="document">
+<h3 align="center">Here is what's happening...</h3>
+<div align="center" class="current-quickie">
+        <a target="_blank" href="http://usegalaxy.org/cloud"><img src="http://galaxy.psu.edu/welcome_img/welcome_images.001.png" width="300" height="200"></a>
+        <a target="_blank" href="http://bitbucket.org/galaxy/galaxy-central/wiki/ISMB2010_GalaxyTutorial_3_RunningYourOwn"><img src="http://galaxy.psu.edu/welcome_img/welcome_images.002.png" width="300" height="200"></a>
+		<a target="_blank" href="http://main.g2.bx.psu.edu/u/aun1/p/ismb2010-demo"><img src="http://galaxy.psu.edu/welcome_img/welcome_images.003.png" width="300" height="200" /></a>
+		<a target="_blank" href="http://bitbucket.org/galaxy/galaxy-central/wiki/DataLibraries/Tutorial/DataLibrariesSampleTracking"><img src="http://galaxy.psu.edu/welcome_img/welcome_images.004.png" width="300" height="200" /></a>
+		<a target="_blank" href="http://main.g2.bx.psu.edu/u/aun1/p/windshield-splatter"><img src="http://galaxy.psu.edu/welcome_img/welcome_images.005.png" width="300" height="200" /></a>
+</div>
+
+<h3 align="center">Live Quickies</h3>
+
+<div class="previous" id="previous">
+        <table border="0" cellpadding="0" cellspacing="0" width="100%">
+            <tr>
+                <td>
+                    <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie1_TabSeq/flow.html',width:640,height:480,scroll:'no'})">
+	                   <div class="quickie">
+                        <img src="images/qk/quickie1_small.png" border="0">
+	                   </div>
+                    </a>
+                </td>
+                <td>
+                    <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie2_Grouping/flow.html',width:640,height:480,scroll:'no'})">
+	                   <div class="quickie">
+                        <img src="images/qk/quickie2_small.png" border="0">
+	                   </div>
+                    </a>
+                </td>
+                <td>
+                    <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie3_Intervals/flow.html',width:640,height:480,scroll:'no'})">
+	                   <div class="quickie">
+                        <img src="images/qk/quickie3_small.png" border="0">
+	                   </div>
+                    </a>
+                </td>
+                <td>
+                    <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie4_whatsNew/flow.html',width:640,height:480,scroll:'no'})">
+	                   <div class="quickie">
+                        <img src="images/qk/quickie4_small.png" border="0">
+	                   </div>
+                    </a>
+                </td>
+                <td>
+                    <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie5_join/flow.html',width:640,height:480,scroll:'no'})">
+	                   <div class="quickie">
+                        <img src="images/qk/quickie5_small.png" border="0">
+	                   </div>
+                    </a>
+                </td>
+                <td>
+                    <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie6_share/flow.html',width:640,height:480,scroll:'no'})">
+	                   <div class="quickie">
+                        <img src="images/qk/quickie6_small.png" border="0">
+	                   </div>
+                    </a>
+                </td>
+                <td>
+                    <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie7_sr_beta/flow.html',width:640,height:480,scroll:'no'})">
+	                   <div class="quickie">
+                        <img src="images/qk/quickie7_small.png" border="0">
+	                   </div>
+                    </a>
+                </td>
+                <td>
+                    <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie8_solid_single_end/flow.html',width:640,height:480,scroll:'no'})">
+	                   <div class="quickie">
+                        <img src="images/qk/quickie8_small.png" border="0">
+	                   </div>
+                    </a>
+                </td>
+                <td>
+                    <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie9_solid_mate_pair/flow.html',width:640,height:480,scroll:'no'})">
+	                   <div class="quickie">
+                        <img src="images/qk/quickie9_small.png" border="0">
+	                   </div>
+                    </a>
+                </td>
+                <td>
+                    <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie10_custom_genome/flow.html',width:640,height:480,scroll:'no'})">
+	                   <div class="quickie">
+                        <img src="images/qk/quickie10_small.png" border="0">
+	                   </div>
+                    </a>
+                </td>
+                <td>
+                    <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie_11_illumina_se/flow.html',width:640,height:480,scroll:'no'})">
+	                   <div class="quickie">
+                        <img src="images/qk/quickie11_small.png" border="0">
+	                   </div>
+                    </a>
+                </td>
+                                <td>
+                    <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie12_illumina_pe/flow.html',width:640,height:480,scroll:'no'})">
+	                   <div class="quickie">
+                        <img src="images/qk/quickie12_small.png" border="0">
+	                   </div>
+                    </a>
+                </td>
+                               <td>
+                    <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie_13_fastq_basic/flow.html',width:640,height:480,scroll:'no'})">
+	                   <div class="quickie">
+                        <img src="images/qk/quickie13_small.png" border="0">
+	                   </div>
+                    </a>
+                </td>
+
+                               <td>
+                    <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie_14_fastq_adv/flow.html',width:640,height:480,scroll:'no'})">
+	                   <div class="quickie">
+                        <img src="images/qk/quickie14_small.png" border="0">
+	                   </div>
+                    </a>
+                </td>
+                <td>
+                    <a href="javascript:parent.show_in_overlay({url:'http://screencast.g2.bx.psu.edu/galaxy/quickie_15_lastz_frag/flow.html',width:640,height:480,scroll:'no'})">
+	                   <div class="quickie">
+                        <img src="images/qk/quickie15_small.png" border="0">
+	                   </div>
+                    </a>
+                </td>
+
+
+
+            </tr>
+      </table>
+</div>
+
+<script type="text/javascript">
+      // Scroll to last quickie in box
+      document.getElementById("previous").scrollLeft = 100000000;
+</script>
+
+<br/>
+<br/>
+<br/>
+<hr/>
+
+<p><a target="_blank" class="reference" href="http://g2.trac.bx.psu.edu/wiki/GalaxyTeam">The Galaxy team</a> is a part of <a target="_blank" class="reference" href="http://www.bx.psu.edu">BX</a> at <a target="_blank" class="reference" href="http://www.psu.edu">Penn State</a>.</p>
+
+This project is supported in part by <a target="_blank" class="reference" href="http://www.nsf.gov">NSF</a>, <a target="_blank" class="reference" href="http://www.genome.gov">NHGRI</a>, <a target="_blank" class="reference" href="http://www.huck.psu.edu">The Huck Institutes of the Life Sciences</a>, and <a target="_blank" class="reference" href="http://www.ics.psu.edu">The Institute for CyberScience at Penn State</a>.
+<p><small>Galaxy build: <b>$Rev 3885:1ab9d6b0ddfc$</b></small></p>
+</div>
+</div></body></html>
--- a/scripts/taxonomy/processTaxonomy.sh
+++ b/scripts/taxonomy/processTaxonomy.sh
@@ -10,5 +10,9 @@ cat gi_taxid_nucl.dmp gi_taxid_prot.dmp 
 echo "Sorting gi2tax files..."
 sort -n -k 1 gi_taxid_all.dmp > gi_taxid_sorted.txt
 rm gi_taxid_nucl.dmp gi_taxid_prot.dmp gi_taxid_all.dmp
+echo "Removing parenthesis from names.dmp"
+cat names.dmp | sed s/(/_/g | sed s/)/_/g > names.temporary
+mv names.dmp names.dmp.orig
+mv names.temporary names.dmp

    